In mass spectrometry, sample molecules are ionized and introduced into a vacuum (or ionized in a vacuum), and mass to charge ratios of target molecular ions are measured by measuring movements of the ions in an electromagnetic field. Since the obtained information represents macroscopic quantities of the mass to charge ratios, it is difficult to obtain information on internal structure by a single mass analysis. Accordingly, a method called tandem mass spectrometry is used. That is, sample ions are isolated or selected in the first mass analysis. These ions are referred to as precursor ions. Subsequently, the precursor ions are dissociated by a certain technique. The dissociated ions are referred to as fragment ions. The dissociated ions are further mass-analyzed, thereby obtaining information on the generation patterns of the fragment ions. Since there is a rule for dissociation patterns depending on each dissociation technique, it is possible to infer the sequence structure of the precursor ions. Particularly, in the fields of analysis of biomolecules composed of protein, adiabatic reactions, such as charged particle reaction, using Collision Induced Dissociation (CID), Infra-Red Multi-Photon Dissociation (IRMPD), and Electron Capture Dissociation (ECD), Electron Transfer Dissociation (ETD), Proton Transfer charge Reduction (PTR), and Fast Atomic Bombardment (FAB), are used for the dissociation technique.
CID is currently widely used in the field of protein analysis. A kinetic energy is provided to the precursor ions to allow them to collide with gas. Molecular vibration is excited by the collision and the molecular chain is dissociated at sites susceptible to cleavage. Further, a method that has recently come to be used is IRMPD. The precursor ions are irradiated by an infra-red laser to allow them to absorb multiple photons. The molecular vibrations are excited and a molecular chain is dissociated at a site susceptible to cleavage. The sites susceptible to cleavage by CID or IRMPD are sites designated as a-x and b-y in the backbone consisting of an amino acid sequence. It is known that a complete structural analysis cannot be carried out only by CID or IRMPD, because even when sites correspond to a-x and b-y, those are sometimes hard to be cleaved depending on the kind of the amino acid sequence pattern. Therefore, a pretreatment using an enzyme or the like is necessary, which hampers high-speed analysis. Further, when CID or IRMPD is used for post-translationally modified biomolecules, side chains involved in the post-translational modification tend to be easily cleaved. Due to facile cleavage of the side chains, it is possible to determine, based on lost mass, molecular species involved in the modification and whether or not it is modified. However, important information on modification sites concerning which amino acids are modified is lost.
On the other hand, ECD, ETD, and the like, which are the adiabatic dissociating methods using an electron, as other dissociation means, are less dependent on an amino acid sequence (as an exception, proline residue with a cyclic structure is not cleaved) and cleave only one c-z site on the backbone of the amino acid sequence. Therefore, a complete analysis of the backbone chain sequence of a protein molecule can be performed only by the mass spectrometric approach. In addition, ECD, ETD, and the like are suitable for research and analysis of post-translational modification owing to its property of hardly cleaving side chains. Therefore, the dissociation techniques of ECD and ETD have attracted particular attention in recent years. CID and IRMPD, ECD and ETD, and the like can be utilized mutually complementarily because they provide different sequence information, respectively.
In the mass spectrometers of an ion trap type, a quadrupole type, or the like, a radio frequency voltage is applied to a three-dimensional ion trap or to multipole electrodes, thereby focusing the ions to their trajectories.
Non-Patent Document 3 describes a principle that ions are focused to their trajectories in the radial direction by an application of a radio frequency voltage with the use of an idea of pseudopotential. The pseudopotential is the one obtained by expressing a potential in the radial direction formed by a radio frequency voltage with such a potential that is formed by a DC voltage. The ion trap using the radio frequency voltage features that ions can be focused and captured regardless of a positive ion or a negative ion.
Non-Patent Document 1 describes an ETD technique inside a radio frequency ion trap. In a structure of three-series of quadrupole ion traps (LTQ mass spectrometer) provided with wall electrodes, positive ions are introduced from one of two input/output ports for ions placed on both sides and then are kept captured, subsequently negative ions are introduced from the opposite port, and both the positive and negative ions enter into a potential generated by an application of a DC voltage. Then, a secondary radio frequency voltage is applied to the quadrupole and the wall electrodes to react the positive ions and negative ions to each other, thereby causing an ETD reaction.
An ECD technique inside the three-dimensional and radio frequency linear ion traps is described in Patent Document 1 and Patent Document 2. Here, there is proposed the ECD technique, in which a magnetic field is applied onto ion trajectories of the three-dimensional ion trap and linear ion trap, and this magnetic field restricts the electron trajectories so as to avoid the heating of electrons. In the configuration using a three-dimensional ion trap, there is proposed a method, in which a magnet is placed inside a ring electrode or outside an end cap, and electrons are introduced from the outside of the ion trap. Moreover, in the configuration using a linear ion trap, there is proposed a method, in which a magnetic field is applied onto the central axis of the linear ion trap, and electrons are introduced from within the magnetic field onto the ion trajectories.
An ECD technique inside a radio-frequency linear ion trap is described in Non-Patent Document 2. Here, there is described the ECD method, in which a magnetic field is applied to the ion trajectories of a linear quadrupole electrode ion trap to restrict the electron trajectories, thereby avoiding the heating of electrons.
Patent Document 3 discloses a method, in which ions are transported using a DC voltage in a fragment device comprising a serially arranged plurality of electrodes. Namely, a potential hill and well are formed with a DC voltage, and ions are pushed out at this potential hill and are captured at this potential well, whereby the ions are transported by transferring the potential hill and potential well. Moreover, by changing an applying method of the DC voltage, the speed of the potential hill and well can be adjusted, and consequently the transporting speed of ions can be adjusted. This approach can adjust the transit time of ions.    Patent Document 1: U.S. Pat. No. 6,800,851 B1    Patent Document 2: US Patent Application Publication No. US 2004/0155180 A1    Patent Document 3: U.S. Pat. No. 6,884,995 B2    Non-Patent Document 1: John E. P. Syka et al., PNAS, vol. 101, No. 26, pp. 9528-9533    Non-Patent Document 2: Takashi Baba et al., Analytical Chemistry, 2004, vol. 76, pp. 4263-4266    Non-Patent document 3: H. G. Dehmelt et al., Adv. At. MolPhys 353 (1967), pp. 53-72